What is "prot"? It doesn't seem to have been defined, and it would not
be surprising if the expected bond were breaking.

As Carlos pointed out, this problem is almost certainly noted in the tleap
output, and it's good to learn what to look for. Another good idea (TM)
is to use the "checkvalidity" command in parmed: it searches for missing
disulfide bonds.

But to developers: this points up two genuine problems with tleap:

1. The output is so voluminous that people understandably have a hard
time reading it.
2. tleap really should quit when errors like this are encounterd. I
understand that this would break some existing scripts, but the
benefits are likely to outweigh the disadvantages.

I suppose I should be the one to attack this, but it would be really great
if someone would step up to the plate (this being World Series time....)
It's really pretty trivial coding to find these and other error messages
and make them fatal. Removing un-needed messages is more of an art, but
is still super-straightforward.